Use pre-existed bwa mem file in the pipeline

[songtaogui]

Hi,

Thank you for this wonderful program.

I have noticed that in the T-lex3 pipeline, the reads were mapped to ref with BWA MEM using default options. So I was wondering that is it OK if I modified the script to skip the BWA MEM step by providing a pre-build bwa-mem.bam file? In that case, should I still provide the reads.fastq? (If the reads.fastq files were only used for bwa mapping, I would like to modify the script to get rid of these options, because I have removed my raw reads.fq after bwa mapping)

Any suggestion would be grateful.

Best wishes,

SongtaoGui

[m-bogaerts]

Hello,

Thank you very much for your interest in T-lex3.

It is ok if you want to modify it to skip BWA MEM, but notice that fastq files are still needed for the Absent module (which uses a different mapper).

Let us know if we can help with any issue.

Thank you.

María